Scaffold step not using allocated number of threads

[aabood]

Hello,

The scaffolding step is only using one thread instead of the 32 threads that I allocated in the command. runPipeline -v -q -d test13 -a spades -m bowtie2 -gFragGeneScan -X lap -c kraken -p 32 -z species -f Abundance,FunctionalAnnotation How do I force the software to use all 32 threads?

Thank you for your time

[skoren]

Not all steps in metAMOS are parallelized. Part of the scaffolding step is parallelized but other parts (the graph simplification) is single-threaded so this is the expected behavior.

[aabood]

Thank you for your quick response. It has been stuck at this step for approximately 240 hours and using only one cpu /bin/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize is this considered normal then?

The size of my data is about 10G and the pipeline has been running for about 12 days. I am a little bit worried since I am trying to use MetAmos on a data set that is 13 times bigger next.